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- PDB-1y2t: Crystal structure of the common edible mushroom (Agaricus bisporu... -

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Basic information

Entry
Database: PDB / ID: 1y2t
TitleCrystal structure of the common edible mushroom (Agaricus bisporus) lectin
Componentslectin
KeywordsSUGAR BINDING PROTEIN / ABL / Agaricus bisporus / lectin / mushroom
Function / homologyFungal fruit body lectin / Fungal fruit body lectin / Cytolysin/lectin / Cytolysin/lectin / Mutm (Fpg) Protein; Chain: A, domain 2 / carbohydrate binding / Sandwich / Mainly Beta / Agaricus bisporus lectin
Function and homology information
Biological speciesAgaricus bisporus (cultivated mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.5 Å
AuthorsCarrizo, M.E. / Capaldi, S. / Perduca, M. / Irazoqui, F.J. / Nores, G.A. / Monaco, H.L.
Citation
Journal: J.Biol.Chem. / Year: 2005
Title: The Antineoplastic Lectin of the Common Edible Mushroom (Agaricus bisporus) Has Two Binding Sites, Each Specific for a Different Configuration at a Single Epimeric Hydroxyl
Authors: Carrizo, M.E. / Capaldi, S. / Perduca, M. / Irazoqui, F.J. / Nores, G.A. / Monaco, H.L.
#1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2004
Title: Crystallization and preliminary X-ray study of the common edible mushroom (Agaricus bisporus) lectin
Authors: Carrizo, M.E. / Irazoqui, F.J. / Lardone, R.D. / Nores, G.A. / Curtino, J.A. / Capaldi, S. / Perduca, M. / Monaco, H.L.
History
DepositionNov 23, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: lectin
B: lectin


Theoretical massNumber of molelcules
Total (without water)32,1402
Polymers32,1402
Non-polymers00
Water3,027168
1
A: lectin
B: lectin

A: lectin
B: lectin


Theoretical massNumber of molelcules
Total (without water)64,2794
Polymers64,2794
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area7560 Å2
ΔGint-20 kcal/mol
Surface area21340 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)91.935, 96.681, 75.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operations: -x, y, 1/2-z

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Components

#1: Protein lectin


Mass: 16069.765 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Agaricus bisporus (cultivated mushroom) / References: UniProt: Q00022
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Sodium formate, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 24, 2002 / Details: Three-segment Pt-coated toroidal
RadiationMonochromator: Double Crystal (Si111, Si220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→74.5 Å / Num. all: 53757 / Num. obs: 53757 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rsym value: 0.047 / Net I/σ(I): 7.9
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 7.1 / Num. unique all: 7606 / Rsym value: 0.087 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
autoSHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 1.5→65.94 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.047 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20298 5466 10.2 %RANDOM
Rwork0.18727 ---
all0.18887 48264 --
obs0.18887 48264 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.461 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2--0.54 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.5→65.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2270 0 0 168 2438
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0212318
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9031.9173148
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9275282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0610.2344
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021808
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1660.2955
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0720.2170
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1120.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0770.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.3061.51400
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.58522264
X-RAY DIFFRACTIONr_scbond_it0.8573918
X-RAY DIFFRACTIONr_scangle_it1.4484.5884
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.206 388
Rwork0.2 3385

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